The relationship between convective penetration depth and tropospheric humidity is central to recent theories of the Madden–Julian oscillation (MJO). It has been suggested that general circulation models (GCMs) poorly simulate the MJO because they fail to gradually moisten the troposphere by shallow convection and simulate a slow transition to deep convection. CloudSat and Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) data are analyzed to document the variability of convection depth and its relation to water vapor during the MJO transition from shallow to deep convection and to constrain GCM cumulus parameterizations. Composites of cloud occurrence for 10 MJO events show the following anticipated MJO cloud structure: shallow and congestus clouds in advance of the peak, deep clouds near the peak, and upper-level anvils after the peak. Cirrus clouds are also frequent in advance of the peak. The Advanced Microwave Scanning Radiometer for Earth Observing System (EOS) (AMSR-E) column water vapor (CWV) increases by ~5 mm during the shallow–deep transition phase, consistent with the idea of moisture preconditioning. Echo-top height of clouds rooted in the boundary layer increases sharply with CWV, with large variability in depth when CWV is between ~46 and 68 mm. International Satellite Cloud Climatology Project cloud classifications reproduce these climatological relationships but correctly identify congestus-dominated scenes only about half the time. A version of the Goddard Institute for Space Studies Model E2 (GISS-E2) GCM with strengthened entrainment and rain evaporation that produces MJO-like variability also reproduces the shallow–deep convection transition, including the large variability of cloud-top height at intermediate CWV values. The variability is due to small grid-scale relative humidity and lapse rate anomalies for similar values of CWV.